Interaction of basic fibroblast growth factor (bFGF) with heparan sulfate proteoglycans (HSPGs) plays an important role in the binding of bFGF to its tyrosine kinase receptor (FGFR). The molecular bases of this interaction were investigated by evaluating the capacity of conventional and selectively desulfated heparins i) to affect the binding of bFGF to FGFR and HSPGs of NIH 3T3 cells transfected with FGFR-1/flg cDNA, ii) to facilitate the interaction of bFGF with a recombinant soluble form of the extracellular domain of FGFR-1/flg (xcFGFR-1), and iii) to protect xcFGFR-1 from tryptic cleavage. 6-O-desulfated (6-O-DS) heparin, but not 2-O-desulfated (2-O-DS) and N-desulfated/N-acetylated (N-DS/N-Ac) heparins, retains the capacity to bind bFGF, as assessed by its ability to inhibit bFGF-binding to cell-associated FGFR-1 and HSPGs. On the other hand, at variance with conventional heparin, 2-O-DS, N-DS/N-Ac, and 6-O-DS heparins are all ineffective in potentiating the binding of bFGF to xcFGFR-1 and protecting xcFGFR-1 from tryptic cleavage. The data indicate that 6-O-sulfate groups are not essential for the interaction of heparin with bFGF but are involved in the interaction with xcFGFR-1. Our findings support the hypothesis that HSPGs modulate the binding of bFGF to FGFR through the formation of a ternary complex in which the glycosaminoglycan chains interact with bFGF via 2-O- and N-sulfate groups and with FGFR also via 6-O-sulfate groups.